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The story is similar to (and even could have been based upon) Star Wars; a princess steals a secret data disk from an evil empire, and she safely smuggles out the information through a robot, but is captured herself. Bomberman is training in his headquarters when news arrives about the princess being captured. Bomberman chases after the Garaden Empire to save the Princess, but the Empire eventually claims back the disks to rebuild their leader, Bagular, whose body was destroyed in Super Bomberman 3.

At first Bomberman travels through four worlds; Planet Bomber, Primus Star, Kanatia Star, and Mazone Star. Each world has its respective boss from the Garaden Empire; Endol, Baruda, Bolban, and Natia and her pet robot Cronus. Within each world, there are three different areas with their own collection of stages. Towards the middle of a world Bomberman encounters Nitros, a mysterious recurring mini-boss similar to Bomberman. While on his adventure Bomberman encounters characters from past games such as Black Bomber and Louie. The basic plot for the first three worlds is that Bomberman chases after Princess Millian only to find that she has been transported to the next world. While on Mazone area three, Bomberman finds Princess Millian safe in a laboratory. She tells him to find the rest of the disks in the next few levels. After giving the disks to Princess Millian, she turns out to be Natia in disguise. Natia then sends the disks needed to rebuild Bagular to the Garaden base. After Bomberman battles Natia and Cronus, he sets out towards Garaden Star.

Within Garaden Star Bomberman battles resurrected forms of the past bosses through the various stages. Midway through the world, Bomberman encounters Nitros for a final battle. After the battle, Nitros snaps out of his brain-washed state, explains himself to Bomberman, shares his power with Bomberman, and then tells him to defeat Bagular for him. At the end of the world, Bomberman encounters the recently resurrected Bagular and engages him in a lengthy final battle. As a final act of desperation, Bagular self-destructs Garaden Star in an attempt to kill Bomberman. The story seems to end here with the destruction of the Garaden Empire and the credits.

However, if a perfect score is achieved on every level and all the Adok bombs are collected, a new cut-scene takes place after the destruction of Garaden Star. A mysterious figure says "Bagular you fool, you lost again!" and suddenly the final world Gossick Star appears. At the end of the second level, Bomberman ascends an elevator to the final battle. There he battles Evil Bomber, possibly the real mastermind of the operation. After defeating Evil Bomber, Bomberman flies away in a ship with Princess Millian and the credits run.

Bomberman Hero controls very differently from Bomberman 64. In Hero, the character can jump, has a life meter, faces tougher bosses, and has the ability to throw bombs farther, thus, making Hero a more platform-oriented experience. There are several different areas to be encountered, each with about five different stages. A unique feature is that it's possible to play with an extra advancement, such as a jet pack or a submarine.

There are also several different types of bombs in addition to the regular ones. Ice bombs turn enemies into a block of ice which can be moved around and used to jump on to get to higher places. Salt bombs only harm slugs, which are invulnerable to all other weapons. Control bombs explode when remotely detonated; a useful ability against certain bosses.

Much of the game's replay value is in the sub-mission of scoring the amount of target points per stage, which awards Bomberman a certain amount of stage points (1 through 5) at the end of each level. You can reenter the stages as often as you like, in order to secure the highest possible score within the stage. Medals are awarded on a per-planet basis, awarded based on the total number of stage points at the planet's completion (red, blue, bronze, silver, and gold). Getting a perfect score on every planet (or rather, a gold medal on each one) will award minigames to be accessed on the options screen. The games include:

Slide Racer: Play through the Crystal Hole level on the Bomber Slider, racing against a snow-man. Beat him and get the record time to win.

Golden Bomber: Bomberman gets the Golden Chip, which allows him to travel underwater with ease. Traverse through three stages to beat the Boss of the Woods.

Treasure Hunt: Princess Millian's ship, which was full of treasure taken from Bagular's base, was shot down at the treasures were scattered all over the six planets. Find them all.

Bomberman Hero received generally mixed reviews from critics and fans alike, though the soundtrack was met with significant praise. GameSpot said, "Despite the uninspired plotline, Bomberman Hero is a rather surprising success. In a departure from Bomberman 64, Bomberman Hero boasts a number of new gameplay features that make this a completely new Bomberman game."[5] In a mixed review, IGN heavily criticized the lack of multiplayer mode, stating, "Nintendo and Hudson serve up a decidedly average 3D Bomberman sequel -- without a multiplayer mode."[6]

Edge criticized the graphics for featuring intrusive distance fog and the same texture pattern, which make it difficult for the player to judge depth. However, the magazine concluded that, as a Japanese platformer, the game should not be overlooked, and favorably compared its rewarding exploration with that of Yoshi's Island.[3]

The game has since been recognized for its unique use of jungle and drum 'n' bass style music, by longtime Bomberman series music producer, Jun Chikuma.